To publicly state (or publish) that the FBI collects evidence in internal investigations of subversion or espionage is a, "duh," moment...a restatement of the obvious (whether or not it is widely known).
On the other hand, if in the course of say, the HANSON investigation, it had been published that, "The FBI has gathered wire, fingerprint, and video surveillance evidence against Robert HANSON," this just might have constituted a disclosure of classified information, even if it was common knowledge that, "The FBI gathers evidence in espionage investigations."
That the NSA collects signals intelligence is another, "no duh." The disclosure of their targeting criteria, methods, techniques and results for a given operation, on the other hand, is not so innocent.
Believe me -- I hate to come down on the side of the NY Times in this case. But the more I read about it, the more I'm convinced that they have done nothing illegal.
It's also interesting to note that the lack of formal warrants in these cases may actually work in their favor. If you have a "target" who is not under formal indictment, is not the subject of a subpoena, and is not the subject of a search warrant, the government may not have much legal recourse if someone exposes the investigation of the target.
For example . . . tipping off motorists on the highway by flashing your headlights to warn them of a speed trap down the road does not constitute obstruction of justice in any way.
Its specific targets CERTAINLY are classified information. The difference, I surmise, between the contested NSA program and FISA is the broad admission that the contested NSA program (policy) includes SOME U.S. people as targets of warrantless surveillance.